sim.sigthr: Simulate a significance threshold for (composite) interval...

In mpMap: Multi-parent RIL genetic analysis

Description

Generate a significance threshold by simulating from the null hypothesis. Phenotypic values for the observed genetic data are simulated to represent data with no QTL, and a genomewide p-value threshold is calculated.

Usage

  sim.sigthr(mpcross, nsim = 100, alpha = 0.05, pindex = 1,
    step = 0, ncov = 0, ...)

Arguments

mpcross	Object of class mpcross
nsim	Number of null datasets to simulate; default is 100
alpha	Significance threshold for QTL p-values
pindex	Index of phenotype (if more than one in dataset)
step	Step size at which to compute the QTL profile. Default is 0, at midpoints of marker intervals
ncov	Number of marker covariates to search for - default is 0 for interval mapping
...	Additional arguments

Value

List with components:

alpha	Input significance threshold
nsim	Input number of simulated datasets
minp	Genomewide minimum p-value for each simulated dataset
thr	Empirical p-value threshold

See Also

mpIM

mpMap documentation built on May 29, 2017, 2:50 p.m.